changeset 38:c08b824e40cc draft

planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 86c0c3bb957558f14e9400171640bf5a5c6605c9

--- a/ImportDataFromMatrix.R	Mon Jun 25 04:11:22 2018 -0400
+++ b/ImportDataFromMatrix.R	Mon Jun 25 05:25:40 2018 -0400
@@ -10,7 +10,6 @@
 ##### Read options
 option_list=list(
 		make_option("--input",type="character",default="NULL",help="rdata object containing eset object"),
-		make_option("--conditions",type="character",default=NULL,help="Text file summarizing conditions of the experiment (required)"),
 		make_option("--normalization",type="character",default=NULL,help="log2 transformation"),
 		make_option("--annotations",type="character",default="NULL",help="rdata object containing eset object"),
 		make_option("--rdataoutput",type="character",default="NULL",help="output rdata object containing eset object"),
@@ -30,18 +29,10 @@
 	stop("input required.", call.=FALSE)
 }
 
-if(is.null(opt$conditions)){
-	print_help(opt_parser)
-	stop("conditions input required.", call.=FALSE)
-}
 
 
 #loading libraries
-suppressPackageStartupMessages(require(GEOquery))
-
 suppressPackageStartupMessages(require(Biobase))
-suppressPackageStartupMessages(require(GEOquery))
-suppressPackageStartupMessages(require(GEOmetadb))
 suppressPackageStartupMessages(require(limma))
 suppressPackageStartupMessages(require(jsonlite))
 suppressPackageStartupMessages(require(affy))
@@ -60,13 +51,13 @@
 dir.create(result.path, showWarnings = TRUE, recursive = FALSE)
 
 data=as.matrix(read.table(file = dataFile,row.names=1,header=TRUE))
-conditions=read.table(file=conditionsFile,sep = "\t",row.names=1)
+#conditions=read.table(file=conditionsFile,sep = "\t",row.names=1)
 htmlfile=readChar(result.template, file.info(result.template)$size)
 
-colnames(conditions)=c("source_name_ch1","description")
-phenodata<-new("AnnotatedDataFrame",data=conditions)
+#colnames(conditions)=c("source_name_ch1","description")
+#phenodata<-new("AnnotatedDataFrame",data=conditions)
 
-eset=ExpressionSet(assayData=data,phenoData=phenodata,annotation=annotation)
+eset=ExpressionSet(assayData=data,annotation=annotation)
 
 if (normalization == "quantile") {
 	eset <- normalize.ExpressionSet.quantiles(eset, transfn="log")
@@ -108,4 +99,4 @@
 #writeLines(c("<h2>Venn diagram</h2>"),file.conn)
 #writeLines(c("<img src='venn.png'><br/><br/>"),file.conn)
 #writeLines(c("</body></html>"),file.conn)
-#close(file.conn)
\ No newline at end of file
+#close(file.conn)

--- a/ImportDataFromMatrix.xml	Mon Jun 25 04:11:22 2018 -0400
+++ b/ImportDataFromMatrix.xml	Mon Jun 25 05:25:40 2018 -0400
@@ -4,10 +4,7 @@
 
     <requirements>
         <requirement type="package">bioconductor-biobase</requirement>
-        <requirement type="package">bioconductor-geoquery</requirement>
-        <requirement type="package">bioconductor-geometadb</requirement>
         <requirement type="package">bioconductor-limma</requirement>
-        <requirement type="package">bioconductor-biobase</requirement>
         <requirement type="package">bioconductor-affy</requirement>
         <requirement type="package">bioconductor-affyplm</requirement>
         <requirement type="package">r-jsonlite</requirement>
@@ -26,7 +23,6 @@
         ${__tool_directory__}/ImportDataFromMatrix.R
             --input $input
             --normalization $normalization
-            --conditions $conditions
             --annotations $annotations
             --rdataoutput $result_export_eset
             --htmloutput $result_html
@@ -42,7 +38,6 @@
             <option value="log2">log2 only</option>
             <option value="none">none</option>
         </param>
-        <param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the input file"/>
         <param name="annotations" type="text" label="Annotation GPL code" help="GPL code for annotations"/>		
     </inputs>